Prediction of transmembrane α-helices in prokaryotic membrane proteins: The dense alignment surface method

Miklos Cserzö, Erik Wallin, I. Simon, Gunnar Von Heijne, Arne Elofsson

Research output: Contribution to journalArticle

853 Citations (Scopus)

Abstract

A new, simple method for predicting transmembrane segments in integral membrane proteins has been developed. It is based on low-stringency dot-plots of the query sequence against a collection of non-homologous membrane proteins using a previously derived scoring matrix. This so-called dense alignment surface (DAS) method is shown to perform on par with earlier methods that require extra information in the form of multiple sequence alignments or the distribution of positively charged residues outside the transmembrane segments, and thus improves prediction abilities when only single-sequence information is available or for classes of membrane proteins that do not follow the 'positive inside' rule.

Original languageEnglish
Pages (from-to)673-676
Number of pages4
JournalProtein Engineering
Volume10
Issue number6
Publication statusPublished - Jun 1997

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Membrane Proteins
Proteins
Membranes
Sequence Alignment

Keywords

  • Prokaryotic membrane proteins
  • Transmembrane α-helices

ASJC Scopus subject areas

  • Molecular Biology
  • Biochemistry

Cite this

Prediction of transmembrane α-helices in prokaryotic membrane proteins : The dense alignment surface method. / Cserzö, Miklos; Wallin, Erik; Simon, I.; Von Heijne, Gunnar; Elofsson, Arne.

In: Protein Engineering, Vol. 10, No. 6, 06.1997, p. 673-676.

Research output: Contribution to journalArticle

Cserzö, M, Wallin, E, Simon, I, Von Heijne, G & Elofsson, A 1997, 'Prediction of transmembrane α-helices in prokaryotic membrane proteins: The dense alignment surface method', Protein Engineering, vol. 10, no. 6, pp. 673-676.
Cserzö, Miklos ; Wallin, Erik ; Simon, I. ; Von Heijne, Gunnar ; Elofsson, Arne. / Prediction of transmembrane α-helices in prokaryotic membrane proteins : The dense alignment surface method. In: Protein Engineering. 1997 ; Vol. 10, No. 6. pp. 673-676.
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